Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Anything web-related. Just anything.

    Drupal theme development: where to start

    8th June 2008

    Simplest way to develop your custom Drupal theme is to start with some skeleton/wireframe theme.

    In this post, I’m briefly reviewing 4 themes (atck, blueprint, framework, and zen), made specifically to serve as theme developer’s starting point. All 4 are listed with their features (as per Drupal project page of each one), with my personal “impressions” (not based on actual use experience, yet). There’s also my choice and order of preference for the 4 candidates at the end.
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    Posted in Drupal, Links, Notepad, Software, Web, XHTML/CSS | 8 Comments »

    Ad Unit Guidelines

    7th June 2008

    When either consulting on a new website design, or actually designing one, keep in mind Ad Unit Guidelines if the website is going to use advertising. The list is far not exhaustive, but sufficiently standard.

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    Posted in Links, Notepad, Web, XHTML/CSS | No Comments »

    An alternative to shared hosting

    4th June 2008

    Personal communication resulted in a link to slicehost, who provide VDS/VPS services at prices as low as 20$/mo, which is comparable in price to good shared hosting plans, and is cheaper than Dedicated plans.

    I’m considering a move from shared hosting, and found Slicehost attractive. For 20$/mo, you get guaranteed 256MiB RAM, 10GiB disk and 100GiB traffic, which is sufficient to host several under-1k-per-day sites.

    The only thing which isn’t spoken aloud is the guaranteed CPU speed. Based on the numbers provided: 16GiB total RAM per server, quad-core CPU, and CPU quotas set equivalently to RAM quotas, I came to a conclusion that 20$-plan guarantees ~125MHz of CPU (take 16 GiB, multiply by 4 20$-plans – you get 64 “slices” – virtual servers; quad core CPUs were quoted as 8+GHz – I assume that’s the sum of the core frequencies, thus 8GHz divided by 64 slices gives as little as 125MHz guaranteed per slice).

    The better slice you buy – the more CPU is guaranteed, so for 1024-RAM slice you’d have a minimum of 500MHz of CPU.

    However, slicehost describes their CPU-clamping system as the one allowing “bursted” performance, if others aren’t actively using their CPU shares. So it must be much better than what I’m calculating here. And even if it’s not, then for some applications it’s better to have a 125MHz-clamp on CPU, than have a 20-seconds maximal CPU time limit.

    Still, I’m looking for reasonably-priced collocation services in Ukraine – e.g. those (currently unavailable) from Volia, starting at 40$/mo for the rented physical VIA C7-based server with enough traffic included.

    Update: I now have my own server collocated in Ukraine. This blog still lives on a shared hosting, but I’m considering the move to own server (where I have the biomed half-dead site and resource-hungry COTRASIF tool).

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    Posted in Hardware, Links, Notepad, Web | No Comments »

    COTRASIF: conservation-aided transcription factor binding site finder

    20th May 2008

    With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

    If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

    Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.

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    Posted in Bioinformatics, Links, Science, Software, Web | 6 Comments »

    Flash video in Drupal (links)

    6th May 2008

    Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

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    Posted in CMS, Drupal, Links, Notepad, Software, Web | No Comments »

    NicEdit

    11th April 2008

    NicEdit – lightweight inline configurable rich-text editor for the web. Can fit where both FCKEditor and TinyMCE are too clunky and monstrous.

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    Posted in Links, Notepad, Software, Web | No Comments »

    Spam Karma 2 (SK2) is a life saver plugin

    9th April 2008

    As an update to WordPress anti-spam plugins, I highly recommend Spam Karma 2. For a time, it seems to be the ultimate protection. I turned off all the other anti-spam plugins (including Aksimet), and everything’s just perfect! SK2 gathers up to a thousand spam comments/trackbacks during a single week on this blog, and I never had a complaint from blog visitors on their inability to add a comment (though some did have to fill in captcha to post a comment with links).

    And SK2 still works under WP 2.5! (SK 2.3 was released to support WP 2.1)

    Kudos to Dave!

    It would be a pity if this excellent plugin is abandoned and stops functioning in one of the upcoming WP releases.

    Update: SpamKarma is now GPL (at google code).

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    Posted in CMS, Software, Web, WP PlugIns | No Comments »